Raw sequencing reads were trimmed using a skewer with the following parameter settings: end-quality=15, mean-quality=25, min=30. Trimmed reads were then aligned to the human reference genome GRCh38 using HISAT281 (v2.1.0) using default parameter settings. Gene quantification was performed with htseq-count using the GRCh38 Ensembl v84 gene transcript model. After removing mitochondrial, ribosomal, and lowly expressed genes (those not expressed in at least two samples), we carried out differential expression analyses between paired IL-13-stimulated and control samples (n = 5 donors) and between paired HRV-infected and control samples (n = 5 donors) using the DESeq2 R package (v1.22.2).
Do you have any questions about this protocol?
Post your question to gather feedback from the community. We will also invite the authors of this article to respond.